Awww, shucks.

I’m surprised you got the OTA message – I was under the impression that rooted phones wouldn’t get it. In any case, it’s likely your phone didn’t upgrade properly because it was rooted, but it’s worth checking. (Home screen > Menu > Settings > About Phone > Software. The version should be 2.1update1 if you didn’t get it, 2.2 if you did.

Since you’re getting the OTA now, you could wipe and go back to stock (with S-Off) and let the OTA do it’s thing. Or, S-off, wipe back to stock, and (if you don’t get the OTA right away) use the RUU (ROM Update Utility).

In either case you have to run S-Off and wipe your phone. The RUU is identical to the OTA, so you end up in the same place at the end.

Good luck!